2BIM Dna-Binding Protein date Jan 25, 2005
title Human P53 Core Domain Mutant M133l-V203a-N239y-N268d-R273h
authors A.C.Joerger, A.R.Fersht
compound source
Molecule: Cellular Tumor Antigen P53
Chain: A, B
Fragment: Dna-Binding (Core) Domain, Residues 94-312
Synonym: Tumour Suppressor P53, Phosphoprotein P53, Antigen Ny-Co-13;
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 21 21 21
R_factor 0.180 R_Free 0.223
crystal
cell
length a length b length c angle alpha angle beta angle gamma
64.455 70.992 104.669 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.98 Å
ligand SO4, ZN enzyme
related structures by homologous chain: 1TUP, 2BIO
Primary referenceStructures of p53 cancer mutants and mechanism of rescue by second-site suppressor mutations., Joerger AC, Ang HC, Veprintsev DB, Blair CM, Fersht AR, J Biol Chem. 2005 Apr 22;280(16):16030-7. Epub 2005 Feb 9. PMID:15703170
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (76 Kb) [Save to disk]
  • Biological Unit Coordinates (2bim.pdb1.gz) 37 Kb
  • Biological Unit Coordinates (2bim.pdb2.gz) 37 Kb
  • LPC: Ligand-Protein Contacts for 2BIM
  • CSU: Contacts of Structural Units for 2BIM
  • Likely Quarternary Molecular Structure file(s) for 2BIM
  • Structure Factors (246 Kb)
  • Retrieve 2BIM in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2BIM from S2C, [Save to disk]
  • Re-refined 2bim structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2BIM in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 2BIM
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 2BIM, from MSDmotif at EBI
  • Fold representative 2bim from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2bim_B] [2bim_A] [2bim]
  • SWISS-PROT database: [P04637]
  • Belongs to the pore-forming pnc-27 peptide of 32 aas from the p53 tumor suppressor protein (pnc-27) family according to TCDB.
  • Domain organization of [P53_HUMAN] by SWISSPFAM
  • Alignments of the sequence of 2BIM with the sequences similar proteins can be viewed for 2BIM's classification [P53_HUMAN] at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list.
  • A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification [P53_HUMAN] at ProtoMap. Click on the Cluster number.
  • Other resources with information on 2BIM
  • Community annotation for 2BIM at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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